Jun 9, 2013 10:35 PM

I seem to have been involved in several questions that test or have tested the limits of taxonomy. I have found clear variations or similarities in butterflies. I have been told that they are normal variations within a species, or that they are an abberation within a species, or that they show a subspecies or that it is not clear which species is involved.

So I wonder, more generally, who is the authority that rules over the world of taxonomy (let's say in lepidoptera)? Who authoritatively decides if a variation is one that falls within the bounds of a species, or if it is an abberation within a species, or if it shows a sub-species or if it shows a separate species? And, more importantly, where does this authority specify the differences that definitively mark the boundary between separate species or subspecies? I'd like to know because it has become clear that this information is not in my field guides.

I'll answer, but I hope others will comment, too, as taxonomy itself is subject to opinion!

The authority...

In a sense the authority you are seeking is the scientific community in general, especially the taxonomists and the people who use taxonomy. Down to a certain level of detail, there is usually good consensus (and that is usually where the field guides stop). Below there, at a greater level of detail, there is less consensus - that is, there are more differing opinions on how the natural world should be categorized. Over time, one hopes that continued research and analysis leads to a convergence of opinions - that is, one grey are after another becomes clearer. Such progress is not always smooth, however. For instance the fairly recent advent of DNA typing has shed a new light on many relationships. Many species we had thought to be closely related seem (at least on DNA evidence) to be more distant, and some distantly related species seem to be closer. That can lead to species being moved between genera, for example.

Anyone might publish a paper referring to some organism, and using controversial taxonomy. However, the more learned periodicals operate a system of peer review (perhaps not as unbiassed as one would like to think), so that the more extreme ideas do not make it into print, or only in exceptional circumstances. That helps convergence of opinions.

Regulatory bodies...

On a different level, there are regulatory bodies which provide a consistent set of rules to help taxonomists play by the same rules - how to apply the concepts of family, genus, species, subspecies, forma, varietas, grex, cultivar, etc. The application of those rules to define or redefine individual taxa (and partly by implication the boundaries between them), is down to the skill and choice of individual scientists.

Plants are covered by the International Association for Plant Taxonomy (IAPT), which is working on The International Code of Nomenclature for algae, fungi, and plants - adopted by the 18th International Botanical Congress Melbourne, Australia, July 2011 (http://www.iapt-taxon.org/nomen/main.php).

To some extent, these organizations and their publications provide the ground rules for the kind of criteria to use to decide the range and type of variation in an organism that can be considered a subspecies / forma / varietas / etc.

Now, back to your experiences, Alan...

Inevitably, when an inquirer like you delves into an area of biology or palaeontology deeply enough, he finds grey areas. He has been used to putting organisms into fairly well-defined pigeon holes, and expects no different now. But these deep pigeon holes really are not that well defined for the inquirer, and for four reasons:

1. nature really can be more vague down here (even better-defined organisms are variable to some extent)

2. science has yet to do the work to define the pigeon holes

3. different scientists may define the same pigeon hole in different ways

4. the inquirer may not have the tools and expertise to see the boundaries properly (eg. genital examination under the microscope or DNA profiling or pollen surface analysis)

In this informational environment, the inquirer should be prepared to accept:

- variation exists in almost all organisms, at all levels of detail

- many things are not well known in detail

- off-the-shelf publications may not go into enough detail

- scientific papers and/or their authors may need to be consulted

- opinions may vary between experts

- the inquirer may need to develop new skills and/or tools in order to understand the experts and/or to do their own research

When confronted with an inexact identification, some choices may be available. Suppose you have a butterfly, you are fairly sure of the species, and you think it may be a particular subspecies, but you cannot find a description of how the subspecies differs from the typical species itself. For instance Coenonympha arcania ssp. huebneri.

I think Mike has summed it up nicely - taxonomy, like most science, works on a concensus of opinion and peer review. There are ICZN rules for how zoological species can be named (i.e. literally how you choose a name and how that name is written and revised over time) but there are no rules on what constitues a particular taxon, besides the type description itself and physical comparisson with the holotype.

When someone proposes a species (or subspecies) they should publish an article in a peer-reviewed and reputable journal giving the full name; describing the taxon carefully - how it differs from its peers and as much information about its ecology and distribution as is known. They should then declare a specimen as the holotype and lodge that holotype in a publicly accessible and secure store, like a national museum. The Natural History Museum's most prized posessions are its types because they are literally the specimens upon which a name is based and they can be referred to and compared to subsequent catches to help workers identify material or work on further taxonomic revisions.

Now, that is the ideal scenario because anyone can look up the person who described the taxon (their name and date of publication is part of the fully-qualified name) and track down the exact description of the species (this can be tricky) and then read their explanation of why they chose to split it. But ... and this is the big problem ... not all descriptions are as full and explanatory as others and, especially with the smallest subdivisions (forms, abberations etc.), it can be more variable. I know many neotropical species in my group (Diptera, Tachinidae) where the descriptions are woefully inadequate and the holotypes (if they still exist) are stored 1000s of miles from where I work, so it is virtually impossible at the moment to get a handle on what the author actually meant.

From a UK perspective, I manage the UK Species Inventory - a huge database of the names of all the wildlife that can be found in the UK. When someone proposes that I add some new names to the database I would always ask other experts in that group for confirmation that they were generally accepted as good taxa and that they were really found in the UK. If there was still some debate and the taxonomy was quite radical I would generally stay with what we had and wait until the experts had thrashed it out and reached an concensus.

I have to express some disappointment at discovering that taxonomy is not a science. I am not the only one under that misapprehension – Wikipedia certainly describes it as a science, as do you, Chris. But a science it clearly is not. A science would have clear objective criteria for deciding what constitutes a difference that marks out two separate species, or two separate subspecies and so on. Concensus and peer review is not enough to constitute a science, in my humble opinion.

But it would seem it is more like literary criticism: Shakespeare is considered to be a great author not because there are any objective ways of deciding or measuring the greatness of an author but because most people in the field share that opinion. So butterfly specimens X and Y are from different species, different subspecies, the same species but with an aberration present or simply the same species and showing normal variation, not because there are objective criteria for deciding this but rather it will depend on whether the person discovering specimen Y which appears different from specimen X has sufficient Facebook friends in the world of taxonomy to support his assertion as to what the difference constitutes.

In my opinion, Alan is wrong about natural science and also about literary criticism. If we consider two fundamental laws of nature - that nature is in perpetual motion, and that no individual component of nature can be understood in isolation from its relation to the whole, it becomes clear that a) nature's laws of motion must also apply to 'objective criteria' - these are not carved in stone!, and b) there can be no theoretical definition of an individual sub-species of a butterfly without a theory of butterflies as a whole, of butterflies as a part of the insect kingdom, of insects as part of the evolution of life, and so on. Similarly, there is no science of taxonomy in isolation from the science of biology, physics etc. Science is indivisible!

And this also goes for social science. If it is purely a matter of opinion that Shakespeare is a finer writer than Enid Blyton, then the same goes for all social phenomena, and social science is impossible. Social science differs from natural science in three respects: first, the human brain and human consciousness is more complex than any other natural phenomenon; second, human culture is evolving far more rapidly than any species and right now is changing faster than at any time in history; and third, that when we study human society we are also studying ourselves, and objectivity therefore requires self-knowledge and the extirpation of prejudices, alienation etc. This makes scientific knowledge of society exceedlingly difficult, and maybe we can only ever approximate to it - but to say that it is purely a matter of opinion why the Holocaust happened, or the Iraq war, or the current global crisis, is a counsel of despair.

Taxonomy is an academic discipline that deals with describing and classifying organisms. It may not be a science in itself, but it is certainly as scientific as other branches of biology, which is a science. The subject is complex, so the problems may be difiicult to resolve in clear-cut ways like in physics. That's why biology and socilogy are 'soft' sciences, while chemistry and physics are 'hard' sciences.

Taxonomy and other biological disciplines may rely on consensus of opinion, but that opinion is not based on taste and culture, as in literature, but on empirical evidence. The evidence may be insufficient sometimes, or difficult to collect, but it in principle testable. For example, you can run DNA tests or hybridisation experiments to see if two similar-looking organisms are separate species. IDs based on visually comparing insects or their photos with descriptions and drawings in books may look unscientific, but they are based on the inductive reasoning at the heart of science. It's not perfect, but it works.

Taxonomy has the three attributes of a true science. 1 - it's materialistic (no supernatural forces invoked to explain the phenomena); 2 - it has a coherent theoretical framework supported by various other disciplines - the theory of evolution; and 3 - it is empirically testable. The latter means that you can make predictions such as: insects A and B look very similar, but if we find an area where their distribution overlaps we should find no hybrids, so we can call them good species. That's a testable hypothesys, and the answer can be yes or no, whatever the evidence shows.

Thanks for your answer. I certainly did not wish to suggest that taxonomy is not an academic discipline. But I stick to my assertion that if it is a science then it must be based on objective definitions of what constitutes a difference leading to classifying two species, two subspecies or variations within a species or an abberation. Indeed you go some way towards providing an answer when you say that if insects A and B look similar (and have some differences, implied) and there is an area where both are present and there are no hybrids then they are separate (you used the word 'good') species. That is indeed a testable hypothesis (leaving aside the difficulty of proving the negative hypothesis that no hybrids exist).

Could you expand on this and explain similarly sub-species, abberations and variations within a species? What is the situation when there is no overlap - does that automatically mean separate species?

I agree that much of science ultimately comes down to a concesus of opinion (which is what peer review can amount to), but it should be opinion as to whether a testable hypothesis has been proven.

Alan

PS I did post last year some photos of Iberian marbled whites which clearly had different wing colouration, questioning whether they were sub-species. The answer from the museum expert, and sadly I cannot identify who that was or be sure that what I write next is completely accurate since that thread seems to have disappeared, was to the effect that since the various colourations I illustrated all existed in the same area they could not be indicative of separate species or sub-species! Curiously at odds with the testable hypothesis above.

The definitiion of a species used to be that it was a group of individuals that could breed and produce fertile offspring. While this works for many groups it doesn't work well for a lot of the species we are familiar with and which we hang on to as true species because they have significantly different morphology to their peers.

Some genetic lineages that produce significantly different and stable morphology continue to be able to reproduce with closely related species - perhaps because they are newly created splits and they haven't evolved a means of avoiding hybridisation. It might also be because they have evolved in populations that are separated geographically and so they have only bred within a particular genetic pool. When barriers to them hybridising with their ancient relative are dropped (eg. a natural event happens to bring them together) they might appear morphologically different but they can still hybridise with other species.

Practically speaking, the concept of species is used most effectively to distinguish between genetic lineages that we want to define and protect. Whether they can hybridise is a relatively clumsy tool with which to define a species and we tend to go on significant but stable morphological or (more recently) sometimes genetic differences. But these definitions must allow for some morphological and genetic variability within a species and also simply the fact that it is impossible to come up with a simple rule that applies to all different groups of organism, due to their vastly different morphology

Florin has pretty much hit the nail on the head. Sexual reproduction and genetic mutation in biological organisms creates minute but measurable differences in the DNA of individuals. Humans like to group and pigeon-hole different organisms so that we can explain their relatedess to each other and so that we can have a point of reference when talking about these groups. But the individuals in most species are variable to some extent and they are constantly evolving so it isn't always possible to assign strict morphological rules to how the smaller groupings (species & subspecies etc) are defined - it will always come down to the opinion of experts assessing similarity to the holotype. If we were able to see the DNA easily then I suspect that we could define taxa and give them rules/formulae that relate to the genes common to individuals in a species but as we cannot do this as a matter of routine taxonomy we rely on morphology, which is reliable enough but not always as easy to define.

It's a slightly tongue-in-cheek observation but the only 'correctly' identified specimen of any species if the holotype - the one that the name was given to and the individual that was described by the original author. All subsequent identifications are opinions of individuals ... which is why an identification is always dated and the determiner's name is attached to it so that other workers can judge how accurate the identification might be and so they can contact the determiner to discuss the identification if necessary (assuming they are still live!). Other experts might offer alternative identifications and it is up to the person working on the material to decide which taxonomy he goes with and which determination he accepts.

Thanks. I agree there are always small differences arising in DNA - this leads to evolution. Beneficial changes persist and less useful changes die out (according to Darwin, or is that Wallace?). I'm not sure that seeing the genome would make it any easier as I don't suppose there are separate genes that define phylum, class, family, genus etc. And how many molecular difference would there have to be between two DNA strands?

Florin has provided a testable hypothesis for determining if two creatures that look similar but different constitute separate species. And that was basically what I was asking about - the criteria for deciding if differences amount to different species, subspecies etc. I am fairly comfortable with the idea that putting such criteria into operation will rely on a concensus of opinion.

Your latest reply raises a completely new question. The only correctly identified specimen is the one originally used to identify a new species. It's a bit like saying the only true kilogram is the one preserved in a museum in Paris (except that I think that standard was replaced some time ago). Does this mean, that to identify a new species it is necessary to physically catch and preserve a specimen? I ask because I thought that catching wild creatures is now frowned upon. Indeed, if there is a new butterfly species out there it must be rare because nobody else has seen it yet, in which case to catch a specimen could be a criminal act (tongue slightly in cheek here).

I will let Florin come back on the first bits and have a go at answering your last question, regarding practical taxonomy and identification.

Collecting specimens of most organisms isn't frowned upon if it is done responsibly for scientific research and not purely for personal pleasure or beautification. The only time that it might be frowned upon is when you are dealing with very small, isolated populations, of usually higher animals such as birds or mammals that have very slow rates of reproduction. All the entomologists that I know of collect responsibly - I don't know anyone who actually enjoys the act of killing something but we do accept that to do fundamental research into biodiversity we do often need to take specimens.

There are many reasons why taking specimens might be necessary - off the top of my head:

1. To actually identify the majority of species you do need to examine them under a microscope and you often need to dissect specimens to be able to see things like genitalia etc. Butterflies and the majority of moths are fairly easy to identify alive, in a box, but the majority of the ~7000 flies or ~7200 wasps in the UK have very similar relatives and so you have to be extremely careful with your identifications to make sure that they are correct. A matter of a few bristles or a couple of ridges in the carapace can indicate a completely different species.

Most experts will retain all the specimens, for reference purposes - the books aren't always as clear as they could be and it helps a lot to have pre identified material to hand. Also, we regularly look back and check our identifications and reevaluate them in light of new keys or new revisions suggested by other experts.

As a recording scheme organiser I am often sent specimens of flies to have their identifications checked and confirmed. This is very important - especially with the rare species - to make sure that we really do understand their distributions and can learn about their ecological requirements. With this information we can advise the decision-makers and hopefully make sure that species are protected from having their habitats destroyed by unsympathetic changes in land use.

2. Taxonomy changes quite frequently and what was thought to be 1 species of fly in 1930 might turn out to be 5 species in 2013 - as researchers understand biodiversity better they often find cryptic species. Without specimens collected across many decades we wouldn't be able to go back in time to reidentify material and learn how past populations have changed.

I am also personally very grateful to the collectors of old because we can go back through their collections and examine the data labels pinned to their specimens. This tells me where and when each specimen was collected and we can go back to those old localities and look to see if they still exist there. Sadly, in many cases the habitats have been changed drastically but in quite a lot of cases we have been able to confirm that a rare species is hanging on and we can raise its profile to highlight the importance of protecting particular habitats or simply pieces of land that they rely on.

3. To act as types - we have already chatted a bit about the concept of species descriptions and their holotypes. Without a specimen to define the species it becomes very difficult to fix a concept. In the case of some of the extremely rare and isolated higher animals I think good photographs have recently been accepted fairly widely as evidence of a new species. But most insects are distinguished using morphology that isn't readily visible while alive and moving about.

I should add that the reason that photos might be accepted for mammals and birds is primarily because they reproduce very slowly and taking specimens might significantly affect the population if it is very small - and if something that big hasn't been discovered yet then it must have a fairly restricted population. But insects reproduce very quickly (often many generations per year) and experiments have been done to show that the sampling of one or two individuals really has no measurable impact on a population. There are also very few experts working on them and so the number of entomologist "predators" pales into insignificance when compared to the natural predation they suffer every day.

I hope that explains a bit about the issue of taking specimens - do ask away if you have more questions

If we could leave the world of butterflies for a moment and move to something we are all more familiar with I'd like to take the example of domestic dogs. We all know that dogs come in a number of pedigree breeds and these have a clearly different morphology. Nobody could mistake an old English sheepdog for a Yorkshire terrier or a bulldog for a dachshund. Even reduced to a skeleton, these are clearly different. We also know that left to their own devices these dogs will interbreed and create hybrids so I guess from Florin’s definition these all have to be considered the same species.

But given the clearly different morphologies of the pedigree breeds, what does a taxonomist make of these? Are they sub-species? I know that these breeds were created artificially by humans through selective breeding but that is no different from cultivated flowers, all of which seem to be accorded their own Latin species/subspecies identifiers. Then again, some of these breeds come in different but limited colour schemes. West Highland terriers are always all-over white but boxer dogs can be either tan or brindle (either of which may have attractive white trims to add individuality). What does a taxonomist make of such colour schemes?

You make some good points - breeds of domesticated animals were something that fascinated Darwin and he studied them for many years with a view to seeing whether inherritence in breeds would give him an insight into the mechanism in wild animals. My own view is that they are not really a good example because the breeds are kept artificially distinct (while retaining the ability to cross back into other breeds) by very unnatural selection, quite unlike what happens in the wild. But I take your point that in a broad sense they are different genetic lineages that are the same species but are still morphologically very different.

We call them 'breeds' because they are domesticated animals but in wild animals they might be called 'varieties' or 'subspecies'. Broadly speaking (and completely off the top of my head) a 'species' remains distinct even in geographical areas that overlap with related species; while 'subspecies' tend to be morphologically different from the parent species but are also geographically isolated from them. Varieties or forms tend to be common morphological types that crop up within colonies of the parent species. So if you have a species of Blue butterfly there might be a colony of it isolated in a different valley that has evolved a slightly different wing pattern and this would usually be a subspecies unless someone thought that it was so different that it warranted being called a species. However, if you take the Silver-washed Fritillary, they often turn up darker individuals and these are called varieties.

But I would encourage you not to get too hung-up on the exact rank that is associated with a taxonomic group because it can be misleading. Different types of organism can be grouped in different ways (insects, fungi, plants etc) and using different criteria (morphology or DNA) and some taxonomists prefer finer while other prefer broader subdivisions - whether to use genera and/or subgenera can be a hot topic of debate. But essentially all taxonomists are trying to do is to group life in ways that seem to explain the world around us in a logical way. This takes into account the taxon's ability to hybridise but also takes into account stable morphological differences and sometimes even allows for geographic isolation from their peers. The results are not arbetrary though - I could propose all kinds of rubbish but if it isn't backed by good science and it doesn't convince the other workers in my group then it just won't get accepted - they will just ignore it and continue with the current taxonomy.

If I examine a species of fly and, after careful consideration, I believe that it really comprises the existing species plus a hidden/cryptic species then I have to prove that it is a genuine, stable morphotype. I would examine a lot of specimens taken across the geographic range of the species (and across years of collecting) and check that my morphological differences are not just a continual gradation or variation - I should be able to confidently split the existing specimens into one or other species by stable features. I might also be able to back up my assertion by showing that the 2 species have slightly different distributions but they overlap in some areas, while remaining distinct.

Sorry, probably rambling a bit but it's been a long day ... I'm off for my dinner

Taxonomy is an inexact science, as has been said. Many divisions – especially below about the level of family - rely on fairly arbitrary criteria, but they should still be based on genuine scientific data.

Genetic comparison would seem at first glance to be the way to go; but it seems to have at least as many practical pitfalls as observation and cross breeding experiments.

Comparing the whole genome of a large number of organisms would be an impossible task, at least at present. Therefore only comparatively small sections of the genome have to be chosen for study – but which sections??? Some non-vital parts of the genome (such as those coding for colour) are far more variable than others. Should differences in those genes be given equal weight as less variable genes? If not, how should they be weighted?

The choice of DNA sampling may be affected by human bias – the scientists’ personal beliefs and assumptions influencing which sections of the genome are chosen. For example, early studies claimed about 98% similarity between chimp and human DNA. But the choice of DNA to compare was based on the assumption (which might or might not be true) that humans and chimps are closely related. The parts of the genome tested reflected that assumption. It has since been shown (using more representative DNA sampling) that the actual similarity is much less – especially in the Y chromosome.

Of course, since a chimp’s body structure and other aspects of its biology are similar to humans it would seem reasonable whatever the explanation for it, to expect more similarities than would be found between a human and a mouse, or a cat and a mouse. But to assume that chimp and human DNA has to be very similar and slant the studies to “prove” what one already firmly believes to be true is not good scientific method!

Gene studies may even throw up some unexpected results in that area. For example, one study appeared to show that horses are more genetically similar to bats than they are to cows; and a large part of the human genome is surprisingly similar to that of kangaroos!

“Junk DNA” is another example of assumptions affecting the results, and perhaps taxonomic studies based on them. It was assumed initially that non protein coding regions of DNA had no function; so these were ignored in early research. More recent studies have shown that most of this DNA (thought at first to be composed mainly of useless evolutionary leftovers) is very active and must therefore have a function. Indeed, several inherited disorders in humans have been shown to be linked to this part of the DNA. Some non-coding regions are now known to be involved in switching genes on or off, as required, or determining the point at which the chromosome begins to be “read”, and the direction; so that one gene can be used to make a number of different proteins.

The idea that most science has to be precise and accurate is just not true; but it is still useful, as long as we try to set aside our biases and preconceived ideas - or at least be aware of and make allowances for them.

Thanks Drosophila. I think you are echoing my own thoughts above, that looking at DNA will not be the answer to the difficult questions of taxonomy.

Turning to your last sentence, it is certainly a mistake to think that science has to be accurate (or reflect the truth is another way of putting that) or precise. All science is about building models that help us understand the world. I still think a science should be guided by testable objective criteria, not a democracy of who gets the most support. I liked Florin's definition of a "good species" but I'm disappointed that this cannot be extended to other levels of taxonomy, in particular the lower levels: if separate species can be defined objectively by such a test then the grouping into higher levels is one of convenience and a question of which grouping builds the most useful model but if there is no way to objectively define lower levels then what purpose do they serve?

We use science to describe and explain the world around us. It is the most accurate and truthful explanation we have but no scientist would ever say that his theory would be the ultimate explanation. There are always alternate views and, as we learn more, we discover better ways to explain things.

Taxonomy is the science that we use to group and explain relatedness of different organisms but these groupings are actually fairly unnatural. Individuals are the tips of unique genetic lineages and are not all clones so they do not fit comfortably into neat little boxes. But these artificial groupings do serve a purpose - they allow us to measure biodiversity and they give us points of reference when doing research. Also, taxonomy is flexible enough to apply to diverse groups, from algae to whales, and it gains this flexibility from having few hard rules. Instead of a clumsy rule that says what a species is/isn't we have the expert opinion of people who really understand the diversity of the group (ie. they know how individuals in that group are currently grouped), and this is moderated by peer review.

I like that explanation. Chris - a cross between a summary and a definition of what taxonomy is and what it does.

Not sure about the last sentence though;I am suspicious of peer review as it is so open to being dominated by the views of the majority, who may not always be correct. It has happened and is still happening, (though maybe not so much in taxonomy) that a vocal and powerful majority may sneer at, shout down, withold funding or even actively exclude those of differing views; even if there are good empirical reasons to suggest the latter may be correct.

For example, Galileo's view (backed up by empirical observations) that the earth revolved around the sun was at first opposed most strongly by his fellow scientists, not the Church as is popularly supposed (the Church just jumped on the scientists' bandwaggon). And Louis Pasteur's elegant experiments disproving "spontaneous generation" (abiogenesis) also met with stiff resistance from his fellow scientists.

As Alan said, "I still think a science should be guided by testable objective criteria, not a democracy of who gets the most support." I agree with Alan that scientific studies should indeed be as objective as possible. Although, as I said, that is not as easy as we may think.

Message was edited by: Drosophila - some additions in the middle paragraph.

I think peer-review has probably moved on a bit since Galileo's day - or I would like to hope so! But in general I would agree that it depends on the peers being open to new ideas, as long as they are backed by good science.

A teacher or researcher, however well qualified scientifically, who throws doubt on the Big Bang or (especially) its connected concept of Evolution still gets opposition. Ridicule, being ignored, not getting research published, loss of funding, even loss of one's job may result.

The Big Bang sounds like a fairy tale to me. Yet it is considered scientific fact:

Yet science is by its nature unable to deal with the question of origins. We can only study things in the here and now and put forward hypotheses on how what we observe may have come about. Whether it did actually happen that way is a historical question, impossible to prove or disprove through science alone. The most we can do scientifically is to examine possible alternatives and try to decide which is more likely.

As I said before, our beliefs, biases and starting assumptions affect our science. If the former are wrong, our conclusions will probably be wrong too. For example,assuming evolutionary relationships has sometimes hindered scientific progress. I mentioned above the flaws in chimp DNA studies and the delay in realising that non-coding DNA, far from being "junk" has an important range of purposes.

I don't agree that science is unable to deal with the question of origins and you yourself said that science can "put forward hypotheses on how what we observe may have come about". All science is about putting forward hypotheses (or theories, or ideas, if you prefer) that can be tested by experiment and that can be refined when that hypothesis is found to be flawed in some way (whether they are hypotheses about now, the future or the past).

When we discover a multitude of galaxies all moving away from each other at speeds proportional to their separation it is a perfectly legitimate question to ask how they got into that position and to "run the video backwards" using known laws of physics. In the same way when Darwin and Wallace thought to question how the observed biodiversity could have arisen, and especially given the peculiarities of the Galapagos and the Wallace line, it is legitimate science to propose a mechanism for this even if it seems impossible to go back in time to test it. (In fact I believe ways of testing the hypothesis have been found using species that reproduce at a great rate, such as fruit flies.)

Anyway, there are far bigger problems with the Big Bang than the idea of nothing giving rise to everything. I think we agree, however, that peer review does have dangers that can impede the progress of science as well as having the benefits of weeding out poor science, cranks and frauds.

“I don't agree that science is unable to deal with the question of origins and you yourself said that science can "put forward hypotheses on how what we observe may have come about". All science is about putting forward hypotheses (or theories, or ideas, if you prefer) that can be tested by experiment and that can be refined when that hypothesis is found to be flawed in some way (whether they are hypotheses about now, the future or the past).”

Perhaps I should have said “Science is unable to deal with the question of ultimate origins.”

What I strongly object to is when a particular (in my opinion very poor) hypothesis becomes the ruling paradigm, set in stone as far as the majority is concerned and assumed to be fact. Whatever tests, observations and experiments are performed that show it is highly unlikely to be true, the central belief is still held regardless, and discrepancies explained away. Other hypotheses, however reasonable and however closely they fit the observations and scientific testing, don’t have a hope of being accepted.

In fact you would probably (though you may be too polite to say so!) rate me among the “poor scien[tists], cranks and frauds” that need to be weeded out!

...Re: taxonomy, what do we actually observe?

We see large groupings of living things that have similar characteristics to each other but unlike the characteristics of any other group. Between these large groupings there are large gaps and very few, and often disputed, “missing links”. Fossils of a given group of organisms are usually easily recognised as virtually identical to modern forms rather than some intermediate or poorly developed version on its way to becoming something else. Breeding experiments show that beyond a certain point further genetic change is impossible if the organism is to remain viable.

However, at genus, species and sub species level (or even sometimes at family level) there is no need to search for “missing links”, they are everywhere, making the taxonomist’s job difficult, as we have seen. This strongly suggests that many of these smaller taxonomic groupings did indeed diversify from a common ancestor.

So we have two things happening or having evidence that they happened in the past:

1. Organisms have adapted and diversified, apparently from an original basic kind, producing new genera, species and sub-species.

2. There were/are a number of these basic kinds of organism but very little, if any, evidence that they were ever related to or derived from any other basic kind.

There is also the problem of abiogenesis, which goes against the known laws of physics, chemistry and biochemistry. You may have heard of the “Origin of Life Prize” brought out several years ago, that sets out strict guidelines and a reward for anyone who can show scientifically how this could have happened. It is still unclaimed, and in my opinion is unkely to ever be.

Yet nearly everyone believes, in spite of the evidence, that life just appeared all by itself and gradually became more and more complex.

I should have said "Breeding experiments in higher animals show that beyond a certain point further genetic change is impossible if the organism is to remain viable." Prokaryotes such as bacteria have a different genetic organisation. They are apparently less subject to genome deterioration and "error catastrophe" in a population, because fatal genetic changes are usually weeded out at once, instead of being retained as often happens in higher organisms. Their fast rate of reproduction and biochemical variability helps too.

To further explain, here are three versions of the "tree of life" model:

Version A is the classical idea of all living things having a direct, common ancestor, with the tips of the branches representing genera. species and sub species . B is a more complecated recent hypothesis with several interlocking "branches". But C is the only one there is empirical evidence for.

The creosote bush is a modern example of diagram A This is a picture of the one considered the oldest, "King Clone". It looks like many individual bushes but it is in fact one individual plant derived from one seed. The connections have died away to give the impression of a number of individuals. By contrast, there is a wooded are behind my house. If I was unable to go there and had no access to any other information I might think the whole mass of trees were actually one plant. Instead it is more like diagram C, many separate plants of different types, arising from different seeds.

I think my point would be that, from genetics, we now understand that individuals within species are not identical to each other. We can't apply strictly defined labels to the groupings because nature just isn't that convenient. What we can do is to group taxa that are related into groups that scientists can relate to and work with - e.g. from kingdom down to subspecies. Those boxes are sometimes very clear cut but for others there is more debate and there is still a huge amount of work to be done to refine them.

The tree of life is one way to express our understanding of evolution and it is true that a lot of the placement of fossils is conjecture. But that's not bad - it's actually completely compatible with good science. We don't have to see or touch an electron to deduce that it exists - likewise with chemical formulae - they are our best explanation for the world we see around us. The same logic and reasoning actually applies outside science in that we also don't have to have met Napoleon Bonaparteto be quite sure that he existed. There are countless paintings, eyewitness accounts and artifacts that allow historians to research what went on in the past.

It's not at all unreasonable to assume that DNA-based organisms are related to each other and that if you analyse that DNA the relative similarities in the code will show you the relatedness of those taxa. Results have repeatedly supported what taxonomists for years deduced from morphology.

Science is about coming up with a hypothesis; reasoning what we would see if the hypothesis was correct; then performing experiments to compare the hypothesis against reality. If someone comes up with a better idea of how life evolved then I think all taxonomists would be really interested to hear it. But those ideas can't just be conjecture - they have to be based on good, repeatable science otherwise they won't be accepted because we have a pretty good theory at the moment that seems to explain what we see. It isn't perfect but to date nobody has come up with a sound alternative that convinces enough experts

I agree with most of what you say, but not the assumption behind your reasoning - the assumption that evolution has to be true because it’s the best/only explanation we have.

For example, “Relatedness” in itself is not evidence for evolution. Otherwise (if we didn’t happen to know better) we might make a convincing case for a Rolls Royce being descended from a bicycle (via the motorbike and Robin Reliant)!

“Good, repeatable science” does support the idea of a limited form of common descent within a basic kind of organism. But beyond that the evidence suggests another factor at work.

Possible explanations for “Relatedness” are:

1. Common descent (as with the mesquite bush)

2. Common design (as with the bike and motor car)

I personally believe that both of these are seen in living things; but that examples of common descent arise from designed variability.

However, design needs a designer by definition, and most present day scientists don’t want to be convinced of that particular “sound alternative”

Florin’s definition of science near the beginning of this discussion shows this bias, because it specifically excludes any “supernatural” input.

Of course empirical scientific methods cannot investigate the supernatural as such. But neither is there any rational scientific reason for denying the possibility of a “supernatural” explanation of origins.

Prof Richard Lewontin – more honest than most - admitted his own personal bias in this area:

‘We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfil many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories,becausewe have a prior commitment, a commitment to materialism.

“It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, thatmaterialism is an absolute, for we cannot allow a Divine Foot in the door.”

“Materialism is an absolute, for we cannot allow a Divine Foot in the door.” Why not? What is he afraid of? Whyshould it be thought “unscientific” to allow for the possibility of a causeless Cause (aka God) as the ultimate origin of everything???

The Biblical account of origins is fully consistent with what we observe in the here and now. In taxonomy we see a number of distinct and separate groups of living things, varying within the group yet still "according to their kind" (dogs don’t give birth to kittens, and an apple tree doesn’t produce strawberries).

To say with Lewontin that “We take the side of science”, then admit that science has nothing to do with what we believe is completely illogical!

Evolution is only a “pretty good theory that seems to explain what we see” if you are already convinced it’s true. To me it’s a pretty poor hypothesis born of attempts to exclude God!

Anyway I've said enough for one discussion, and probably gone off topic too.

I think we're digressing way too far and, to be honest, I don't think that I am qualified to debate the various rights and wrongs of a person's faith vs the theory of evolution by natural selection. But I will respond with my own views and there I think we should probably leave it to others ;-)

Basically, we see evolution happening all around us - via slight changes in the DNA of organisms ranging from bacteria to oak trees. Mutations happen all the time and when organisms reproduce asexually they 'stir the DNA pot' each time with (usually) unique outcomes. If Darwin had been able to analyse DNA in the 1800s then I would suggest that he would have published "The Origin of Species" far sooner than he did because it is an absolute killer explanation of how organisms pass on traits to their offspring.

We can also reason that the pressures of trying to survive and reproduce would favour those organisms that have a configuration that gives them the edge over others - natural selection. Once we accept that evolution through natural selection happens and has happened (as is proven by what tiny fraction of the fossil record survives) then it doesn't really need a deity to make the process continue. I can't say that gods don't exist because maybe there are supernatural beings looking down on us but I just don't see any evidence that they *do* exist and I certainly don't see them as a necessary component of the processes we can see being acted out around us every day.

I believe that you could suggest that a deity was present at the time of the big bang or that they created that 'spark of life' that created the first living being (though in the latter I think this has been explained chemically). But once we had DNA-based life-forms I don't believe that you would need a deity to explain what we see around us now. It doesn't need a god to give life a helping hand over the difficult bits and it doesn't need a supernatural being to steer it either ... the process of evolution through natural selection just goes ahead. I understand that the odds of beneficial mutations happening can sometimes seem incredibly small but so is winning the lottery and yet people do win it every week ... 14-million to 1 odds played out over time and with millions of rolls of the metaphorical dice and someone's numbers do come up.

Anyway, I'd be interested to hear more from the OP on whether they are happy with the concept of speciation and taxonomy in general but I think we should put the origins of life and other topics to bed - it's interesting but not really for this forum ;-)

I delayed replying because of trying (in vain!) to resist the temptation to argue! Also as you say it is off topic; although fairly relevant to taxonomy because most taxonomists assume evolution is true (in the sense of all life being interrelated by common descent etc) and use that assumption as a basis for their work.

It is very irritating to be constantly told that evolution is “science” and “faith” isn’t. This is actually a case of “the pot calling the kettle black”. I am not asking anyone to debate “faith vs science” but to think for yourself re questions of science, instead of having blind faith in evolution

My scepticism re Evolution has nothing to do with my personal faith as such; although the latter provides an alternative worldview that fits the scientific facts well. In fact for a long time I believed in Evolution as well as God.

You are also making the usual mistake of confusing two separate things (one with plenty of evidence that it is a fact, the other with none) and calling both “Evolution.” The evidence you provided for “evolution” all falls into the first category, not the second.

For example, natural selection etc can easily produce new species (which is again relevant to taxonomy). But it is not a mechanism for evolution because selection is, by definition, choosing from what is already present. By contrast, evolution from supposedly simple organisms to more “advanced” requires masses of brand new and extremely complex information to be inserted into the genome in fully integrated and fully operative form. What we now know about the complexity of DNA operation shows that this would almost certainly be impossible by mere natural means, however gradually it might be claimed to happen over millions of years.

Anyway, we will have to start a new thread to take this any further. Or post me privately, instead of replying on this thread and starting me off again (I can resist anything except temptation, as someone said!!! :-D)

I also suffer for not being able to take part in a conversation that I would normally enjoy. I think I could make some useful remarks on some of your (both) posts, but I don't have the time with many enquiries here in the AMC. Plus this deserves a different place that the ID Forum.

The email addresses are all private. I checked, but there is no way to see anything other than your own email, and you don't have the option of making it public. You can always email us at ias2@nhm.ac.uk if you prefer, or visit us in the Museum to chat about such subjects. I'm new to this field - philosophy of science - but I like it.